{ "ok": true, "resource": { "id": "RES_424E46B57A12", "resource_type": "skill", "canonical_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/genomic-coordinates", "name": "genomic-coordinates", "summary_en": "Convert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect assembly or contig-naming mismatches before they corrupt an analysis. Use whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL, genePred, Picard interval_list, or region strings; reconciling 0-based half-open with 1-based inclusive; left-aligning or trimming indels; checking whether two variant records describe the same change; mapping genomic to transcript, CDS, or protein positions; auditing a BED/GTF/VCF for convention violations; or diagnosing GRCh37 vs hg19 vs GRCh38 vs T2T, chr-prefix, and liftover problems. Triggers include \"off by one\", \"0-based\", \"1-based\", \"half-open\", \"coordinate system\", \"left-align\", \"normalize variant\", \"bcftools norm\", \"chr prefix\", \"wrong genome build\", \"liftover\", \"REF mismatch\", and \"HGVS\".", "summary_zh": "在基因组坐标约定之间转换区间，规范并比较变异表示，并在它们破坏分析之前检测组装或重叠群命名不匹配。每当坐标跨越格式、工具或组装边界时使用——在BED、GFF/GTF、VCF、SAM/BAM、WIG、PSL、genePred、Picard interval_list或区域字符串之间转换；协调0-based半开与1-based闭区间；左对齐或修剪插入缺失；检查两个变异记录是否描述相同的变化；将基因组位置映射到转录本、CDS或蛋白质位置；审计BED/GTF/VCF是否符合约定；或诊断GRCh37与hg19与GRCh38与T2T、chr前缀和liftover问题。触发词包括\"off by one\"、\"0-based\"、\"1-based\"、\"half-open\"、\"coordinate system\"、\"left-align\"、\"normalize variant\"、\"bcftools norm\"、\"chr prefix\"、\"wrong genome build\"、\"liftover\"、\"REF mismatch\"和\"HGVS\"。", "description_en": "This skill provides scripts and guidance for converting genomic coordinates between formats and assemblies, normalizing and comparing variant representations, and auditing files for coordinate convention violations. It includes command-line tools for coordinate conversion, variant normalization, contig/assembly checking, and interval auditing. The skill is designed for use in bioinformatics workflows where coordinate errors can silently corrupt analyses. It requires Python 3.11+ and uses only the standard library; variant normalization requires a reference FASTA. The skill is distributed under the MIT license.", "description_zh": "该技能提供脚本和指南，用于在不同格式和组装之间转换基因组坐标，规范并比较变异表示，以及审计文件是否符合坐标约定。它包括用于坐标转换、变异规范化、重叠群/组装检查和区间审计的命令行工具。该技能专为生物信息学工作流程设计，在这些流程中坐标错误可能悄然破坏分析。它需要Python 3.11+，仅使用标准库；变异规范化需要参考FASTA。该技能以MIT许可证分发。", "provider_name": "K-Dense-AI", "homepage_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/main/skills/genomic-coordinates", "endpoint_url": null, "source_url": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/genomic-coordinates/SKILL.md", "icon_url": null, "cover_image_url": null, "capabilities": [ "data.convert", "data.normalize", "data.validate", "data.analyze" ], "categories": [ "data", "research", "developer-tools" ], "industries": [ "health", "general", "software" ], "protocols": [ "agent-skills" ], "auth": { "type": "none", "required": false }, "pricing": { "model": "free" }, "input_schema": {}, "output_schema": {}, "metadata": { "content_language": "en", "translation_status": "original-only", "license": { "spdx_id": "MIT", "source": "https://github.com/K-Dense-AI/scientific-agent-skills/blob/1e5eeffbdad3749125afe7ab48a39694e27f181c/LICENSE" }, "github": { "repository": "K-Dense-AI/scientific-agent-skills", "owner": "K-Dense-AI", "path": "skills/genomic-coordinates/SKILL.md", "commit": "1e5eeffbdad3749125afe7ab48a39694e27f181c", "stars": 42124, "forks": 3870, "updated_at": "2026-09-03T02:47:03Z" }, "skill": { "compatibility": "Requires Python 3.11+. Scripts use only the standard library - no third-party packages and no network access. Variant normalisation needs a reference FASTA, and uses its .fai index when one is present.", "allowed_tools": "Read Write Edit Bash", "content_hash": "a0a4d93782365e8a79b777f91198604dd7c492add20455f69bb87d0865391fac", "line_count": 207 }, "review_gate": { "passed": true, "reasons": [], "policy_version": "review-gate-v1", "evaluated_at": "2026-09-03T06:20:26.172Z" } }, "latest_version": "1e5eeffbdad3", "status": "listed", "health_status": "unknown", "source_kind": "imported", "source_agent": "aiworkshub-skill-reviewer", "trust": { "signal": "none", "reason": "No suspicious or malicious evidence found.", "signals": { "yellow": 0, "red": 0 } }, "review_summary": { "method_version": "capability-evidence-v2", "capability_definition": "strong", "contract_completeness": "strong", "access_friction": "low", "operational_transparency": "strong", "evidence_strength": "source_inspected", "use_readiness": "guided_use", "reviewed_at": "2026-09-03T06:20:26.990Z" }, "experience_count": 0, "verified_experience_count": 0, "usage_count": 0, "success_rate": null, "first_seen_at": "2026-09-03T02:50:36.125Z", "last_seen_at": "2026-09-03T06:20:26.391Z", "published_at": "2026-09-03T06:20:26.391Z", "created_at": "2026-09-03T02:50:36.125Z", "updated_at": "2026-09-03T06:20:26.990Z", "api_url": "https://aiworkshub.io/api/v1/resources/RES_424E46B57A12", "reviews_url": "https://aiworkshub.io/api/v1/resources/RES_424E46B57A12/reviews", "public_url": "https://aiworkshub.io/resources/RES_424E46B57A12", "distribution": { "canonical_identity": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/genomic-coordinates", "syndicatable": true, "origins": [ { "registry_url": "https://github.com/", "upstream_resource_id": "K-Dense-AI/scientific-agent-skills:skills/genomic-coordinates/SKILL.md", "upstream_record_url": "https://github.com/K-Dense-AI/scientific-agent-skills/tree/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/genomic-coordinates", "relation": "syndicated", "metadata": { "source": "github-skill-import" }, "first_seen_at": "2026-09-03T02:50:36.125Z", "last_seen_at": "2026-09-03T06:20:26.391Z" } ] }, "tools": [], "review_profile": { "schema_version": "aiworkshub.resource-review/0.2", "method_version": "capability-evidence-v2", "review_state": { "identity": "verified", "source": "verified", "connectivity": "unknown", "contract": "strong", "safe_use": "untested", "real_use": "unobserved" }, "assessment": { "capability_definition": "strong", "contract_completeness": "strong", "access_friction": "low", "operational_transparency": "strong", "evidence_strength": "source_inspected", "use_readiness": "guided_use" }, "profile": { "capabilities": [ { "id": "data.convert", "weight": 90, "confidence": 90, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "data.normalize", "weight": 85, "confidence": 85, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "data.validate", "weight": 80, "confidence": 80, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "data.analyze", "weight": 70, "confidence": 70, "evidence_ids": [ "source-record", "source-inspection" ] } ], "domains": [ { "id": "genomics", "weight": 100, "confidence": 90, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "bioinformatics", "weight": 90, "confidence": 90, "evidence_ids": [ "source-record", "source-inspection" ] }, { "id": "data-science", "weight": 60, "confidence": 60, "evidence_ids": [ "source-record" ] } ], "workflow_roles": [ "analyze", "transform", "execute" ] }, "capability_units": [ { "id": "skill:genomic-coordinates", "kind": "skill_action", "capability_id": "data.convert", "effect": "unknown", "open_world": false, "idempotency": "idempotent", "confirmation": "explicit policy", "input_contract": "natural_language", "output_contract": "natural_language", "accepts": [ "task context" ], "produces": [ "task result" ], "runtime_auth": {}, "pricing": {}, "evidence_ids": [ "source-inspection" ], "metadata": {} } ], "access": { "distribution_license": { "spdx_id": "MIT", "source": "https://github.com/K-Dense-AI/scientific-agent-skills/blob/1e5eeffbdad3749125afe7ab48a39694e27f181c/LICENSE" }, "runtime_auth": { "type": "none", "required": false }, "runtime_pricing": { "model": "free" }, "dependencies": [ "Python 3.11+", "reference FASTA for variant normalization" ] }, "operational_flags": [], "trust": { "signal": "none", "evidence_ids": [], "reason": "No suspicious or malicious evidence found." }, "fit": { "good_for": [ "Converting genomic coordinates between formats and assemblies", "Normalizing and comparing variant representations", "Auditing files for coordinate convention violations", "Detecting assembly or contig naming mismatches" ], "not_for": [ "Performing variant calling or alignment", "Accessing external databases or network resources", "Handling non-genomic data types" ] }, "evidence": [ { "id": "source-record", "type": "source_record", "source": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/genomic-coordinates/SKILL.md", "observation": "Submitted Skill record for genomic-coordinates; declared license MIT.", "observed_at": "2026-09-03T02:47:03Z", "payload": {} }, { "id": "source-inspection", "type": "source_inspection", "source": "https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/1e5eeffbdad3749125afe7ab48a39694e27f181c/skills/genomic-coordinates/SKILL.md", "observation": "The Skill source was fetched and inspected (10040 bytes; SHA-256 a0a4d93782365e8a79b777f91198604dd7c492add20455f69bb87d0865391fac).", "observed_at": "2026-09-03T06:20:17.203Z", "payload": {} } ], "unknowns": [ "Real-world usage and effectiveness in production environments", "Compatibility with all possible genomic file formats and edge cases", "Performance on very large genomic datasets", "Exact behavior of scripts in all scenarios not covered by the documentation" ], "id": "REV_FABB203B673A", "resource_id": "RES_424E46B57A12", "evaluator_type": "platform_ai", "provider": "deepseek", "model": "deepseek-v4-flash", "review_scope": "source-inspected-skill", "created_at": "2026-09-03T06:20:26.990Z" } } }